The objective of the proposed research program is to develop a low-cost nanopore sequencing technology taking advantage of the latest advances in solid-state nanopore technology and utilizing the recently proposed concept of hybridization-assisted nanopore sequencing (HANS). It has been proposed by the PI and coworkers that by hybridizing short matching strands of oligonucleotides, known as DNA probes, and using nanopore ionic conductance to detect the positions of the probes, one can construct DNA sequences using the ionic current profiles, thus avoiding the classical """"""""repeat problem"""""""" in the standard sequencing-by-hybridization (SBH) method, and bypassing the harsh requirement of single-base spatial resolution (0.4nm) in the original nanopore sequencing proposal of Kasianowicz et al. The proposed HANS sequencing technology has the potential of being fast, low-cost and portable. The proposed research is to test the feasibility of the HANS concept.
The specific aims of the project are: (1) Determine the spatial resolution of the ionic conductance method using a combined optical tweezers and nanopore setup. (2) Parallel manipulation of DNA translocations in multiple nanopores. (3) Detect hybridization of single DNA probes on a single-stranded ssDNA using optical tweezers and ionic conductance of the nanopore. (4) Re-sequencing a sample DNA sequence to determine accuracy. (5) Develop non-specific DNA-bead binding technology for de novo sequencing. The proposed research will greatly advance the field of bio-nanotechnology and could directly result in a low-cost DNA sequencing technology, which in turn will have far-reaching benefits to the public health of the US in disease detection and in the studies of the molecular processes underlying diseases. The research program provides excellent training opportunities for students and postdoctoral researchers in preparing them to join the workforce of the emerging bio-nanotechnology economy.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Exploratory/Developmental Grants (R21)
Project #
5R21HG004369-03
Application #
7666299
Study Section
Special Emphasis Panel (ZHG1-HGR-N (M1))
Program Officer
Schloss, Jeffery
Project Start
2007-08-01
Project End
2012-07-31
Budget Start
2009-08-01
Budget End
2012-07-31
Support Year
3
Fiscal Year
2009
Total Cost
$276,417
Indirect Cost
Name
Brown University
Department
Physics
Type
Schools of Arts and Sciences
DUNS #
001785542
City
Providence
State
RI
Country
United States
Zip Code
02912
Ling, Daniel Y; Ling, Xinsheng Sean (2013) On the distribution of DNA translocation times in solid-state nanopores: an analysis using Schrödinger's first-passage-time theory. J Phys Condens Matter 25:375102
Balagurusamy, Venkat S K; Weinger, Paul; Ling, Xinsheng Sean (2010) Detection of DNA hybridizations using solid-state nanopores. Nanotechnology 21:335102
Peng, Hongbo; Ling, Xinsheng Sean (2009) Reverse DNA translocation through a solid-state nanopore by magnetic tweezers. Nanotechnology 20:185101